本节我们继续来进行基因家族数据可视化的第3节教程，通过ggplot2绘制一个富有美感的基因结构图&蛋白保守结构域图，喜欢的小伙伴欢迎关注，多多支持，
原文链接：https://mp.weixin.qq.com/s/k1Mtmf5GKI43SdB_DBG7yg
加载R包
pacman::p_load(ggstar,ggtree,treeio,aplot,tidyverse,
hablar,patchwork,gggenes,ggseqlogo,magrittr)
自定义数据
colors <-c("#E41A1C","#1E90FF","#FF8C00","#4DAF4A","#984EA3",
"#40E0D0","#FFC0CB","#00BFFF",
"#FFDEAD","#EE82EE","#00FFFF")
可视化基因结构图
gene结构信息，可以通过gff文件获取
p <- read.delim("gene.xls",header = T) %>%
as_tibble() %>% convert(num(V2,V3,V4)) %>%
convert(fct(V5))
V1 type V2 V3 V4 V5
1 A02 exon 8000346 8000409 1 TA1
2 A02 exon 8000797 8000922 1 TA1
3 A02 exon 8001037 8001152 1 TA1
4 A02 exon 8001242 8001330 1 TA1
5 A02 exon 8001448 8001493 1 TA1
gene <- ggplot() +
geom_gene_arrow(data=p,aes(xmin = V2, xmax = V3, y = V5,
forward =V4 ,fill = type),
arrowhead_height = unit(3,"mm"),
arrowhead_width = unit(0.8, "mm"))+
geom_segment(data=p,aes(x = V2, xend = V3, y = V5, yend =V5)) +
facet_wrap(~ V5, scales = "free", ncol = 1) +theme_genes()+
scale_fill_brewer(palette="Set2")+
theme(axis.text.x = element_blank(),axis.ticks.x=element_blank(),
axis.text.y=element_blank(),legend.title = element_blank())+
labs(x=NULL,y=NULL)
gene
可视化蛋白保守结构域图
保守结构域文件可通过pfam_scan.pl软件将蛋白序列文件与pfam数据库进行比对获得，命令如下
pfam_scan.pl -fasta pep.fa -dir ~/data/pfam/ -outfile pro.xls
pro <- read.delim("pro.xls",header = T,sep="\t") %>%
as_tibble() %>% convert(fct(gene)) %>%
ggplot(aes(xmin = start,xmax = end,y=gene,fill = type)) +
scale_fill_manual(values = colors)+
geom_gene_arrow(arrowhead_height = unit(3, "mm"),
arrowhead_width = unit(0, "mm"))+
theme_genes()+ylab(NULL)+
theme(legend.title = element_blank(),axis.text.y=element_blank())
pro
patchwork进行图片拼接
pp2 <- gene + pro +plot_layout(ncol =2,width = c(2.5,2))+
plot_layout(guides = 'collect')
pp2
此处应该也将进化树拼接上去，为了方便我进行了省略，有需要的可以自行进行添加